Agilent Technologies, Inc. v. Affymetrix, Inc.

• Decision Date: 04 June 2009
• Docket Number: No. 2008-1466.,2008-1466.
• Citation: 567 F.3d 1366
• Parties: AGILENT TECHNOLOGIES, INC., Plaintiff-Appellant, v. AFFYMETRIX, INC., Defendant-Appellee.
• Court: U.S. Court of Appeals — Federal Circuit

567 F.3d 1366

AGILENT TECHNOLOGIES, INC., Plaintiff-Appellant, v. AFFYMETRIX, INC., Defendant-Appellee.

No. 2008-1466.

United States Court of Appeals, Federal Circuit.

June 4, 2009.

Thomas H. Jenkins, Finnegan, Henderson, Farabow, Garrett & Dunner, L.L.P., of Washington, DC, argued for plaintiff-appellant. With him on the brief was Tina E. Hulse, of Palo Alto, CA.

Stephen C. Holmes, Dewey & LeBoeuf LLP, of East Palo Alto, CA, argued for defendant-appellee. With him on the brief were Barbara A. Caufield, and Michael J. Malecek.

Before MAYER, RADER, Circuit Judges, and POSNER, Circuit Judge.^*

RADER, Circuit Judge.

The United States District Court for the Northern District of California reviewed an interference action that Agilent Technologies, Inc. (Agilent) brought under 35 U.S.C. § 146 against Affymetrix, Inc. (Affymetrix). The district court sustained the decision of the Board of Patent Appeals and Interferences (the Board) and awarded priority to Affymetrix. Agilent Techs. v. Affymetrix, Inc., No. C-06-05958 (N.D.Cal. June 13, 2008) (SJ Order). Because the district court erred with regard to claim construction, improperly denied Agilent's motion for summary judgment with regard to written description under § 112 ¶ 1, and improperly granted Affymetrix's cross-motion on the same issue, this court reverses.

I.

This case arises out of an interference proceeding, No. 105,285, between Agilent and Affymetrix. The claims at issue originated in Agilent's "Schembri" patent, U.S. Patent No. 6,513,968, which claims priority to an application filed August 21, 1998.

After Agilent's Schembri patent issued on February 4, 2003, Affymetrix, believing it had earlier invented the claimed methods, copied the Schembri claims into its "Besemer" application, U.S. Patent Application No. 10/619,244, to provoke an interference. The Besemer application claims priority, through a long string of continuations, to an application filed June 7, 1995. The Board declared an interference on February 16, 2006 to determine which party had priority of inventorship. Because the Besemer application claims the benefit of an earlier filing date, the Board declared Affymetrix the senior party to the interference under 37 C.F.R. § 2.96. Agilent thus had the burden to show prior entitlement to its patented technology.

The disputed claims pertain to "microarray hybridization," a technique for performing multiple genetic analyses on a small fluid sample. Using this technique, a testor can perform millions of genetic tests in a single small assay. A microarray is a solid substrate (e.g., a glass slide) bearing millions of molecular probes. These probes are generally short DNA sequences that bind (hybridize) to specific targets. To conduct a microarray test, the testor introduces a fluid sample containing the genetic material of interest onto the microarray surface. The fluid contacts the probes. The probes then bind to their fluid targets, revealing the presence of those hybridized targets on the microarray. To achieve proper hybridization results, the testor must make sure that the fluid contacts the entire microarray surface. The disputed invention focuses primarily upon the method of mixing the fluid for thorough contact with the microarray surface.

The interfering subject matter in this appeal is claim 20 of the Schembri patent, or claim 66 of the Besemer application. The invention claims a method for mixing a fluid sample during hybridization:

A method comprising:

providing a first substrate and a second substrate having inner surfaces that define a closed chamber therebetween, said chamber adapted to retain a quantity of fluid so that the fluid is in contact with both inner surfaces, and wherein at least one of said inner surfaces is functionalized with polynucleotides, polypeptides, or polysaccharides;

introducing a fluid containing a plurality of components into the closed chamber so as to provide a quantity of fluid therein in contact with both inner surfaces;

providing a bubble in the fluid; and

moving a bubble within the fluid to result in mixing.

Schembri Patent col. 10 ll.33-45, Besemer Application at 39.

A. Schembri's Disclosure of Fluid Mixing

Agilent's Schembri patent discloses a method of conducting a hybridization reaction in a closed chamber. The method forms a bubble in the fluid, and then moves the bubble to cause mixing. According to the Schembri specification, conventional mixing methods (rapidly shaking or rocking fluid in a container) do not adequately mix (or test) assays with small fluid samples. In these situations, where the fluid forms a mere film with a thickness of a few microns, the capillary strength of the fluid often exceeds the forces generated by shaking or rocking. In that case, incomplete mixing compromises the rate, extent, and percentage yield of the hybridization reaction. Schembri claims a new method of mixing fluid via nucleation of bubbles within the film of liquid.

NOTE: OPINION CONTAINING TABLE OR OTHER DATA THAT IS NOT VIEWABLE

Figure 1, above, shows an apparatus with a closed chamber sandwiched between a first substrate 10 and second substrate 11. As seen in the cross-sectional view of Figure 4, DNA probes are attached to the inner surface 12 of substrate 10. The second substrate 11 forms a closed reaction chamber due to the seal 15 between the surfaces. The testor then introduces a fluid sample with DNA targets into the closed chamber 16. The invention then forms a bubble that moves in response to heat resistors 13 inside the chamber. A controller creates this temperature gradient by systemically switching on and off. These temperature changes cause the bubble to move and mix the fluid sample in the closed chamber.

B. Besemer's Disclosure of Fluid Mixing

Affymetrix's Besemer application, entitled "Bioarray Chip Reaction Apparatus and its Manufacture," describes microarray chips and "chip packages" onto which chips are mounted. The chip package serves as a "sealed thermostatically controlled chamber in which fluids can easily be introduced, a practical medium for sequencing by hybridization...." Besemer Application at 2. Figure 3 illustrates a chip packaging device:

NOTE: OPINION CONTAINING TABLE OR OTHER DATA THAT IS NOT VIEWABLE

The invention mounts a microarray chip above the cavity 310. Inlets 350 and 360 communicate with cavity 310 such that "fluids are circulated through the cavity via inlets 350 and 360." Id. at 9.

The Besemer application discloses three embodiments, called "agitation systems," for mixing fluid through the cavity during hybridization. Figures 28 and 30 represent particular embodiments that circulate fluid through the chip package. For purposes of this appeal, these "circulator" embodiments are not materially different. The embodiment in Figure 28 illustrates this mixing technology:

NOTE: OPINION CONTAINING TABLE OR OTHER DATA THAT IS NOT VIEWABLE

The hybridization chip and cavity 310 attach to containers 2810 and 2820. These containers hold fluid targets for hybridization with probes on the chip. Agitator 2801 holds a gas, e.g., nitrogen. Using ports, vents, and valves, the agitator injects gas into the containers in an alternating manner, thereby forcing fluid into and out of the cavity 310. As the fluid flows in and out of the cavity 310, the targets and probes mix to effect hybridization. Notably, in the discussion of this embodiment, Besemer teaches that "[t]he bubbles formed by the N₂ agitate the fluid as it circulates through the system." Id. at 28.

The embodiment in Figure 29, the "vortexer" system, accomplishes fluid mixing in a different manner:

NOTE: OPINION CONTAINING TABLE OR OTHER DATA THAT IS NOT VIEWABLE

This embodiment mounts a hybridization chip package on vortexer 2910. Container 2930 then fills with fluid containing targets. At that point, various valves open to allow nitrogen gas from 2901 to enter container 2930, thereby forcing fluid into the cavity 310. The valves then seal fluid in the cavity and the vortexer vibrates the chip package "similar to a paint mixer" at 3000 cycles per minute. Id. at 29. This motion mixes the targets in the fluid, completing the hybridization reaction.

II.

Before the Board, Agilent filed a single substantive preliminary motion challenging the validity of the copied claims on the grounds that the Besemer application did not describe the invention adequately under § 112 ¶ 1 to show actual possession of the bubble-mixing invention. After a hearing, the Board ruled that Agilent did not prove that the Besemer application lacked adequate written description to support the count (the interfering claims). Schembri v. Besemer, Interference No. 105,285, 2006 WL 2230013 (B.P.A.I. June 28, 2006) (Board Decision). Because it found that the Besemer application showed support for the claimed invention, the Board awarded priority to Affymetrix's application and cancelled the contested claims of Agilent's Schembri patent.

Agilent sought review of this decision by filing a complaint in the Northern District of California under 35 U.S.C. § 146. The parties submitted new expert reports and testimony from their respective expert witnesses. In April 2008, the district court held a claim construction hearing. The court also entertained cross motions for summary judgment on the written description issue. Soon after, the district court granted Affymetrix's motion for summary judgment that the Besemer application satisfies the written description requirement, thereby affirming the Board. The instant appeal challenges the trial court's claim construction and written description decisions. This court has jurisdiction over Agilent's appeal under 28 U.S.C. § 1295(a)(1).

III.

This court must first decide as a legal matter which specification to consult when construing a claim whose written description is challenged in an interference. The district court construed the disputed claims in light of the host application whose written...